Merge pull request #51 from EliotRagueneau/master

Use OLS4

pom.xml

@@ -72,12 +72,12 @@
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-web</artifactId>
-            <version>5.2.22.RELEASE</version>
+            <version>5.3.29</version>
         </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-context-support</artifactId>
-            <version>5.2.22.RELEASE</version>
+            <version>5.3.29</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/cache/OntologyCacheService.java

@@ -6,9 +6,8 @@
 import uk.ac.ebi.pride.utilities.ols.web.service.model.Identifier;
 import uk.ac.ebi.pride.utilities.ols.web.service.model.Term;
 
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.HashSet;
 import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 
 @Service

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/model/FieldList.java

@@ -3,7 +3,7 @@
 /**
  * @author olgavrou
  */
-public class FieldList {
+public class FieldList implements Joinable {
 
     private String iri;
     private String label;
@@ -13,12 +13,12 @@ public class FieldList {
     private String ontologyPrefix;
     private String description;
     private String type;
-    private String synonyms;
+    private String synonym;
     private String score;
     private String ontologyIri;
     private String isDefiningOntology;
 
-    private FieldList(String iri, String label, String shortForm, String oboId, String ontologyName, String ontologyPrefix, String description, String type, String synonyms, String score, String ontologyIri, String isDefiningOntology) {
+    private FieldList(String iri, String label, String shortForm, String oboId, String ontologyName, String ontologyPrefix, String description, String type, String synonym, String score, String ontologyIri, String isDefiningOntology) {
         this.iri = iri;
         this.label = label;
         this.shortForm = shortForm;
@@ -27,7 +27,7 @@ private FieldList(String iri, String label, String shortForm, String oboId, Stri
         this.ontologyPrefix = ontologyPrefix;
         this.description = description;
         this.type = type;
-        this.synonyms = synonyms;
+        this.synonym = synonym;
         this.score = score;
         this.ontologyIri = ontologyIri;
         this.isDefiningOntology = isDefiningOntology;
@@ -65,8 +65,8 @@ private String getType() {
         return type;
     }
 
-    private String getSynonyms() {
-        return synonyms;
+    private String getSynonym() {
+        return synonym;
     }
 
     private String getScore() {
@@ -77,41 +77,16 @@ private String getOntologyIri() {
         return ontologyIri;
     }
 
-    private String getIsDefiningOntology() {return isDefiningOntology;}
+    private String getIsDefiningOntology() {
+        return isDefiningOntology;
+    }
 
 
     @Override
     public String toString() {
-        StringBuilder fieldList = new StringBuilder("fieldList=");
-
-        if (getIri() != null)
-            fieldList.append(getIri()).append(",");
-        if (getLabel() != null)
-            fieldList.append(getLabel()).append(",");
-        if (getShortForm() != null)
-            fieldList.append(getShortForm()).append(",");
-        if (getOboId() != null)
-            fieldList.append(getOboId()).append(",");
-        if (getOntologyName() != null)
-            fieldList.append(getOntologyName()).append(",");
-        if (getOntologyPrefix() != null)
-            fieldList.append(getOntologyPrefix()).append(",");
-        if (getDescription() != null)
-            fieldList.append(getDescription()).append(",");
-        if (getType() != null)
-            fieldList.append(getType()).append(",");
-        if (getSynonyms() != null)
-            fieldList.append(getSynonyms()).append(",");
-        if (getScore() != null)
-            fieldList.append(getScore()).append(",");
-        if (getOntologyIri() != null)
-            fieldList.append(getOntologyIri()).append(",");
-        if (getIsDefiningOntology() != null){
-            fieldList.append(getIsDefiningOntology()).append(",");
-        }
-
-        return fieldList.toString();
+        return "fieldList=" + this.join();
     }
+
     public static class FieldListBuilder {
 
         private String iri;
@@ -122,17 +97,18 @@ public static class FieldListBuilder {
         private String ontologyPrefix;
         private String description;
         private String type;
-        private String synonyms;
+        private String synonym;
         private String score;
         private String ontologyIri;
         private String isDefiningOntology;
 
         public FieldListBuilder() {
         }
 
-        public FieldList build(){
-            return new FieldList(iri, label, shortForm, oboId, ontologyName, ontologyPrefix, description, type, synonyms, score, ontologyIri, isDefiningOntology);
+        public FieldList build() {
+            return new FieldList(iri, label, shortForm, oboId, ontologyName, ontologyPrefix, description, type, synonym, score, ontologyIri, isDefiningOntology);
         }
+
         public FieldListBuilder setIri() {
             this.iri = "iri";
             return this;
@@ -174,7 +150,7 @@ public FieldListBuilder setType() {
         }
 
         public FieldListBuilder setSynonyms() {
-            this.synonyms = "synonyms";
+            this.synonym = "synonym";
             return this;
         }
 
@@ -188,7 +164,7 @@ public FieldListBuilder setOntologyIri() {
             return this;
         }
 
-        public FieldListBuilder setIsDefiningOntology(){
+        public FieldListBuilder setIsDefiningOntology() {
             this.isDefiningOntology = "is_defining_ontology";
             return this;
         }

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/model/Joinable.java

@@ -0,0 +1,24 @@
+package uk.ac.ebi.pride.utilities.ols.web.service.model;
+
+import java.lang.reflect.Field;
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+public interface Joinable {
+
+    default String access(Field field) {
+        try {
+            field.setAccessible(true);
+            return (String) field.get(this);
+        } catch (IllegalAccessException e) {
+            throw new RuntimeException(e);
+        }
+    }
+    default String join() {
+        return Arrays.stream(getClass().getDeclaredFields())
+                .map(this::access)
+                .filter(Objects::nonNull)
+                .collect(Collectors.joining(","));
+    }
+}

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/model/QueryFields.java

@@ -3,7 +3,7 @@
 /**
  * @author olgavrou
  */
-public class QueryFields {
+public class QueryFields implements Joinable {
 
     private String label;
     private String synonym;
@@ -61,26 +61,7 @@ private String getLogicalDescription() {
 
     @Override
     public String toString() {
-        StringBuilder queryFields = new StringBuilder("queryFields=");
-
-        if (getIri() != null)
-            queryFields.append(getIri()).append(",");
-        if (getLabel() != null)
-            queryFields.append(getLabel()).append(",");
-        if (getShortForm() != null)
-            queryFields.append(getShortForm()).append(",");
-        if (getOboId() != null)
-            queryFields.append(getOboId()).append(",");
-        if (getDescription() != null)
-            queryFields.append(getDescription()).append(",");
-        if (getAnnotations() != null)
-            queryFields.append(getAnnotations()).append(",");
-        if (getSynonym() != null)
-            queryFields.append(getSynonym()).append(",");
-        if (getLogicalDescription() != null)
-            queryFields.append(getLogicalDescription()).append(",");
-
-        return queryFields.toString();
+        return "queryFields=" + this.join();
     }
     public static class QueryFieldBuilder {
 
@@ -96,7 +77,7 @@ public static class QueryFieldBuilder {
         public QueryFieldBuilder() {
         }
 
-        public QueryFields build(){
+        public QueryFields build() {
             return new QueryFields(iri, label, shortForm, oboId, description, annotations, synonym, logicalDescription);
         }
         public QueryFieldBuilder setIri() {

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/model/SearchResult.java

@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+import java.util.List;
+
 /**
  * SearchResult contains summary term information after the query to the ols service.
  *
@@ -18,13 +20,13 @@ public class SearchResult implements ITerm {
     private Identifier iri;
 
     @JsonProperty("short_form")
-    private Identifier shortName;
+    private Identifier[] shortName;
 
     @JsonProperty("obo_id")
-    private Identifier oboId;
+    private Identifier[] oboId;
 
     @JsonProperty("label")
-    private String name;
+    private String[] name;
 
     @JsonProperty("description")
     private String[] description;
@@ -53,6 +55,41 @@ public class SearchResult implements ITerm {
     @JsonProperty("obo_definition_citation")
     private OboDefinitionCitation[] oboDefinitionCitation;
 
+    public Term toTerm() {
+        if (this.name == null) return null;
+        if (!this.obsolete) {
+            return new Term(
+                    this.getIri(),
+                    this.getName(),
+                    this.getDescription(),
+                    this.getShortName(),
+                    this.getOboId(),
+                    this.getOntologyName(),
+                    this.getScore(),
+                    this.getOntologyIri(),
+                    this.getIsDefiningOntology(),
+                    this.getOboDefinitionCitation(),
+                    this.getAnnotation());
+        } else {
+            return new ObsoleteTerm(
+                    this.getIri(),
+                    this.getName(),
+                    this.getDescription(),
+                    this.getShortName(),
+                    this.getOboId(),
+                    this.getOntologyName(),
+                    this.getScore(),
+                    this.getOntologyIri(),
+                    this.getIsDefiningOntology(),
+                    this.getOboDefinitionCitation(),
+                    this.getAnnotation(),
+                    this.isObsolete(),
+                    this.getTermReplacedBy()
+            );
+        }
+    }
+
+
     public String getId() {
         return id;
     }
@@ -70,26 +107,26 @@ public void setIri(String iri) {
     }
 
     public Identifier getShortName() {
-        return shortName;
+        return first(shortName);
     }
 
-    public void setShortName(String shortName) {
-        this.shortName = new Identifier(shortName, Identifier.IdentifierType.OWL);
+    public void setShortName(List<String> shortName) {
+        this.shortName = shortName.stream().map(s -> new Identifier(s, Identifier.IdentifierType.OWL)).toArray(Identifier[]::new);
     }
 
     public Identifier getOboId() {
-        return oboId;
+        return first(oboId);
     }
 
-    public void setOboId(String oboId) {
-        this.oboId = new Identifier(oboId, Identifier.IdentifierType.OBO);
+    public void setOboId(List<String> oboId) {
+        this.oboId = oboId.stream().map(s -> new Identifier(s, Identifier.IdentifierType.OBO)).toArray(Identifier[]::new);
     }
 
     public String getName() {
-        return name;
+        return first(name);
     }
 
-    public void setName(String name) {
+    public void setName(String[] name) {
         this.name = name;
     }
 
@@ -165,7 +202,12 @@ public void setOboDefinitionCitation(OboDefinitionCitation[] oboDefinitionCitati
         this.oboDefinitionCitation = oboDefinitionCitation;
     }
 
-    public Identifier getGlobalId(){
-        return (oboId != null)?oboId:shortName;
+    public Identifier getGlobalId() {
+        return getOboId() != null ? getOboId() : getShortName();
     }
+
+    private static <T> T first(T[] array) {
+        return array != null && array.length >= 1 ? array[0] : null;
+    }
+
 }

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/model/Term.java

@@ -136,6 +136,15 @@ public void setSynonyms(String[] synonyms) {
         this.synonyms = synonyms;
     }
 
+    /**
+     * Support synonym/synonyms name which differ between the different ensdoints
+     * @param synonym
+     */
+    @JsonProperty("synonym")
+    public void setSynonym(String[] synonym) {
+        this.synonyms = synonym;
+    }
+
     public String getOntologyName() {
         return ontologyName;
     }

src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/utils/Constants.java

@@ -10,6 +10,6 @@ public class Constants {
     public static final int TERM_PAGE_SIZE = 1000;
     public static final String REFERENCE_SEPARATOR = ":";
     public static final String OLS_PROTOCOL = "https";
-    public static final String OLS_SERVER = "www.ebi.ac.uk/ols/";
+    public static final String OLS_SERVER = "www.ebi.ac.uk/ols4/";
     public static final String OLS_SERVER_DEV = "wwwdev.ebi.ac.uk/ols/";
 }